ROCHESTER — The Police Commission held a special nonpublic meeting with city officials Thursday, to work out issues having to do with increased compensation for police command staff.

As a result of the meeting, the City Council on Tuesday will vote on whether to appropriate money to fund additional cost items listed in the employment agreement for Police Chief Mike Allen.

The council will also discuss whether to fund salary increases for police command staff at a higher rate than what the council previously appropriated.

Thursday’s meeting, which was cited as nonpublic because of personnel matters, took place between the three commissioners, City Manager Daniel Fitzpatrick, Mayor T.J. Jean, and Deputy Mayor Ray Varney.

Before the meeting, Police Commission Chairman James McManus said he scheduled the session to clear the air between the commission and the City Council.

Previously, there has been a question of whether the city would honor the employment agreement between the Police Commission and Allen, who became the police chief six months ago. While the Police Commission is responsible for setting salaries for police staff, only the City Council has authority to appropriate money for any contracts or agreements, said Varney after Thursday’s meeting.

As per the employment agreement, Allen is receiving a base salary of $95,000. The agreement also states his base salary will increase by $2,000 in December, and by another $2,000 in June.

On Tuesday, the council will vote whether to appropriate the additional salary increases for Allen.

Jean said he could not speculate how the City Council’s vote will go on Tuesday, but said he personally will likely vote in favor of the additional funds, because Allen negotiated his contract with the Police Commission in good faith.

Another contentious topic of conversation has been the merit increases for police command staff — before the budget for this fiscal year was approved, the Police Commission requested that enough money be appropriated so that non-union police command staff can get salary increases of 3.25 percent on average. The funds would be distributed to each command staff member on merit basis.

The City Council, however, only appropriated enough funds in the merit pool to cover an equivalent of 2.5 percent increase for each non-union staff member in the city. Most, but not all, of the non-union city employees are members of police command staff.

In July, the Finance Committee voted to only provide $12,027 toward salary adjustments for police command staff, which was $6,276 lower than what Police Commission requested. The committee also voted to prohibit transferring funds from other Police Department accounts to pay for additional salary increases.

According to McManus, none of the command staff saw increases in salaries so far this year.

Varney, however, said the command staff can have raises based on what is appropriated — an average of 2.5 percent.

“How the Police Commission chooses to distribute those funds is their prerogative,” said Jean.

Varney said that an average of 2.5 percent is what was given to other non-union staff members, who do not work for Police Department.

On Tuesday, the City Council will discuss whether to make a supplemental appropriation of $6,276 to fund salary increases for command staff that the Police Commission established.